{"id":"https://openalex.org/W4408739544","doi":"https://doi.org/10.1186/s12859-025-06105-4","title":"Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval\u00a0-\u00a0Phenotypic inference Evaluation framework","display_name":"Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval\u00a0-\u00a0Phenotypic inference Evaluation framework","publication_year":2025,"publication_date":"2025-03-22","ids":{"openalex":"https://openalex.org/W4408739544","doi":"https://doi.org/10.1186/s12859-025-06105-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/40121479"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06105-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06105-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06105-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06105-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089742224","display_name":"Yasemin Bridges","orcid":"https://orcid.org/0009-0002-1371-3782"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]},{"id":"https://openalex.org/I4210149920","display_name":"William Harvey Research Institute","ror":"https://ror.org/0574dzy90","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079","https://openalex.org/I4210149920"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Yasemin Bridges","raw_affiliation_strings":["William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK. y.bridges@qmul.ac.uk","William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK"],"affiliations":[{"raw_affiliation_string":"William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK. y.bridges@qmul.ac.uk","institution_ids":[]},{"raw_affiliation_string":"William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK","institution_ids":["https://openalex.org/I4210149920","https://openalex.org/I166337079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046218667","display_name":"Vin\u00edcius de Souza","orcid":"https://orcid.org/0000-0003-3961-0247"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vinicius de Souza","raw_affiliation_strings":["European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030245859","display_name":"Katherina G Cortes","orcid":"https://orcid.org/0000-0002-9489-3158"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katherina G. Cortes","raw_affiliation_strings":["School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA"],"affiliations":[{"raw_affiliation_string":"School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064320417","display_name":"Melissa Haendel","orcid":"https://orcid.org/0000-0001-9114-8737"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Melissa Haendel","raw_affiliation_strings":["Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031007073","display_name":"Nomi L. Harris","orcid":"https://orcid.org/0000-0001-6315-3707"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nomi L. Harris","raw_affiliation_strings":["Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA"],"affiliations":[{"raw_affiliation_string":"Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001438691","display_name":"Daniel Korn","orcid":"https://orcid.org/0000-0002-1780-9872"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel R. Korn","raw_affiliation_strings":["Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004032262","display_name":"Nikolaos M. Marinakis","orcid":"https://orcid.org/0000-0002-7078-3253"},"institutions":[{"id":"https://openalex.org/I200777214","display_name":"National and Kapodistrian University of Athens","ror":"https://ror.org/04gnjpq42","country_code":"GR","type":"education","lineage":["https://openalex.org/I200777214"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Nikolaos M. Marinakis","raw_affiliation_strings":["Laboratory of Medical Genetics, National and Kapodistrian University of Athens, 11527, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Laboratory of Medical Genetics, National and Kapodistrian University of Athens, 11527, Athens, Greece","institution_ids":["https://openalex.org/I200777214"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040603724","display_name":"Nicolas Matentzoglu","orcid":"https://orcid.org/0000-0002-7356-1779"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicolas Matentzoglu","raw_affiliation_strings":["Semanticly, 10563, Athens, Greece"],"affiliations":[{"raw_affiliation_string":"Semanticly, 10563, Athens, Greece","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086364805","display_name":"James Alastair McLaughlin","orcid":"https://orcid.org/0000-0002-8361-2795"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"James A. McLaughlin","raw_affiliation_strings":["Samples, Phenotypes, and Ontologies (SPOT), European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK"],"affiliations":[{"raw_affiliation_string":"Samples, Phenotypes, and Ontologies (SPOT), European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002223413","display_name":"Chris Mungall","orcid":"https://orcid.org/0000-0002-6601-2165"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher J. Mungall","raw_affiliation_strings":["Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA"],"affiliations":[{"raw_affiliation_string":"Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035403871","display_name":"Aaron Odell","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aaron Odell","raw_affiliation_strings":["Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053103903","display_name":"David Osumi-Sutherland","orcid":"https://orcid.org/0000-0002-7073-9172"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David Osumi-Sutherland","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK"],"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107981662","display_name":"Peter N. Robinson","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139777","display_name":"Berlin Institute of Health at Charit\u00e9 - Universit\u00e4tsmedizin Berlin","ror":"https://ror.org/0493xsw21","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210139777","https://openalex.org/I7877124"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter N. Robinson","raw_affiliation_strings":["Berlin Institute of Health, Charit\u00e9 - Universit\u00e4tsmedizin Berlin, 10117, Berlin, Germany","Berlin Institute of Health, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, 10117, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Berlin Institute of Health, Charit\u00e9 - Universit\u00e4tsmedizin Berlin, 10117, Berlin, Germany","institution_ids":[]},{"raw_affiliation_string":"Berlin Institute of Health, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, 10117, Berlin, Germany","institution_ids":["https://openalex.org/I4210139777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009950897","display_name":"Damian Smedley","orcid":"https://orcid.org/0000-0002-5836-9850"},"institutions":[{"id":"https://openalex.org/I4210149920","display_name":"William Harvey Research Institute","ror":"https://ror.org/0574dzy90","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079","https://openalex.org/I4210149920"]},{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Damian Smedley","raw_affiliation_strings":["William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK"],"affiliations":[{"raw_affiliation_string":"William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK","institution_ids":["https://openalex.org/I4210149920","https://openalex.org/I166337079"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081977290","display_name":"Julius O.B. Jacobsen","orcid":"https://orcid.org/0000-0002-3265-1591"},"institutions":[{"id":"https://openalex.org/I4210149920","display_name":"William Harvey Research Institute","ror":"https://ror.org/0574dzy90","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079","https://openalex.org/I4210149920"]},{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Julius O. B. Jacobsen","raw_affiliation_strings":["William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK"],"affiliations":[{"raw_affiliation_string":"William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK","institution_ids":["https://openalex.org/I4210149920","https://openalex.org/I166337079"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5089742224"],"corresponding_institution_ids":["https://openalex.org/I166337079","https://openalex.org/I4210149920"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":8.7427,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.9751146,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"87","last_page":"87"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9966999888420105,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.8102459907531738},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7855750322341919},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.6880984902381897},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5802303552627563},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5165714025497437},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5076903104782104},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3738483786582947},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36940592527389526},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3240469694137573},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26791682839393616},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26544660329818726},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17962175607681274}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.8102459907531738},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7855750322341919},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.6880984902381897},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5802303552627563},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5165714025497437},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5076903104782104},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3738483786582947},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36940592527389526},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3240469694137573},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26791682839393616},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26544660329818726},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17962175607681274},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-025-06105-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06105-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06105-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40121479","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40121479","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:ark:/13030/qt3ck3969s","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:bb1e55d7dbdf4cbd8c7b908b67733505","is_oa":true,"landing_page_url":"https://doaj.org/article/bb1e55d7dbdf4cbd8c7b908b67733505","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-18 (2025)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt3ck3969s","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/3ck3969s","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, vol 26, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11929307","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11929307","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06105-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06105-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06105-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408739544.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W2019971954","https://openalex.org/W2100407705","https://openalex.org/W2104549677","https://openalex.org/W2127006085","https://openalex.org/W2246559112","https://openalex.org/W2272951769","https://openalex.org/W2606379926","https://openalex.org/W2620099990","https://openalex.org/W2717403933","https://openalex.org/W2761866254","https://openalex.org/W2770026599","https://openalex.org/W2790756470","https://openalex.org/W2952870794","https://openalex.org/W2953836043","https://openalex.org/W2973006910","https://openalex.org/W3047173169","https://openalex.org/W3105982350","https://openalex.org/W3170139103","https://openalex.org/W3173733146","https://openalex.org/W3205440178","https://openalex.org/W3211623409","https://openalex.org/W4206627019","https://openalex.org/W4210744550","https://openalex.org/W4211138825","https://openalex.org/W4224997429","https://openalex.org/W4225310394","https://openalex.org/W4225616009","https://openalex.org/W4239791848","https://openalex.org/W4282918066","https://openalex.org/W4289028887","https://openalex.org/W4289794327","https://openalex.org/W4384201327","https://openalex.org/W4388616071","https://openalex.org/W4389004870","https://openalex.org/W4395451593","https://openalex.org/W4396222038","https://openalex.org/W4399190259"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W915438175","https://openalex.org/W4230315250"],"abstract_inverted_index":{"PhEval":[0,41],"and":[1,13,19,34,46,67,78],"the":[2,7,36],"standardised":[3,26,68],"test":[4],"corpora":[5],"solve":[6],"issues":[8],"of":[9,38,49,59,70],"patient":[10,29,76],"data":[11,27],"availability":[12],"experimental":[14],"tooling":[15],"configuration":[16,37],"when":[17],"benchmarking":[18,48],"comparing":[20],"rare":[21,61],"disease":[22,62],"VGPAs.":[23,50],"By":[24],"providing":[25],"on":[28],"cohorts":[30],"from":[31],"real-world":[32],"case-reports":[33],"controlling":[35],"evaluated":[39],"VGPAs,":[40],"enables":[42],"transparent,":[43],"portable,":[44],"comparable":[45],"reproducible":[47],"As":[51],"these":[52],"tools":[53],"are":[54],"often":[55],"a":[56,65],"key":[57],"component":[58],"many":[60],"diagnostic":[63],"pipelines,":[64],"thorough":[66],"method":[69],"assessment":[71],"is":[72],"essential":[73],"for":[74],"improving":[75],"diagnosis":[77],"care.":[79]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}